The purpose of this project is to develop methodology for analyzing molecular population genetic data. We have examined the performance of HapMap LD tag SNPs using the resequenced data of the Environmental Genome Project (EGP). We have developed a method for selecting multi-population LD tag SNPs using ethnic-specific data from multiple populations. Haplotype-based methods are under investigation for capturing low frequency SNPs with complete and incomplete reference SNP panels such as EGP and HapMap respectively.